Fix typos and other doc/comment issues, add .idea to .gitignore, and delete…

.gitignore

@@ -37,4 +37,5 @@ Theano.suo
 .ipynb_checkpoints
 .pydevproject
 .ropeproject
-core
+core
\ No newline at end of file
+.idea

doc/extending/optimization.txt

@@ -872,9 +872,9 @@ To understand this profile here is some explanation of how optimizations work:
            0.131s for callback
            time      - (name, class, index) - validate time
 
-      Then it will print, with some additional indentation, each sub-optimizer's profile
-      information. These sub-profiles are ordered by the time they took to execute,
-      not by their execution order.
+  Then it will print, with some additional indentation, each sub-optimizer's profile
+  information. These sub-profiles are ordered by the time they took to execute,
+  not by their execution order.
 
   * ``OPT_FAST_RUN`` is the name of the optimizer
   * 1.152s is the total time spent in that optimizer

theano/compile/function.py

@@ -28,7 +28,7 @@ def function_dump(filename, inputs, outputs=None, mode=None, updates=None,
                   on_unused_input=None,
                   extra_tag_to_remove=None):
     """
-    This is helpful to make a reproducable case for problem during Theano
+    This is helpful to make a reproducible case for problems during Theano
     compilation.
 
     Ex:
@@ -36,13 +36,13 @@ def function_dump(filename, inputs, outputs=None, mode=None, updates=None,
     replace `theano.function(...)` by
     `theano.function_dump('filename.pkl', ...)`.
 
-    If you see this, you where probably asked to use this function to
+    If you see this, you were probably asked to use this function to
     help debug a particular case during the compilation of a Theano
-    function. `function_dump` allows to easily reproduce your
-    compilation without asking any code. It pickle all the objects and
+    function. `function_dump` allows you to easily reproduce your
+    compilation without generating any code. It pickles all the objects and
     parameters needed to reproduce a call to `theano.function()`. This
-    include shared variables and there values. If you do not want
-    that, you can set to replace shared variables values by zeros by
+    includes shared variables and their values. If you do not want
+    that, you can choose to replace shared variables values with zeros by
     calling set_value(...) on them before calling `function_dump`.
 
     To load such a dump and do the compilation:
@@ -53,9 +53,9 @@ def function_dump(filename, inputs, outputs=None, mode=None, updates=None,
     >>> f = theano.function(**d)  # doctest: +SKIP
 
     Note:
-    The parameter extra_tag_to_remove, is passed to the StripPickler used.
+    The parameter `extra_tag_to_remove` is passed to the StripPickler used.
     To pickle graph made by Blocks, it must be:
-    ['annotations', 'replacement_of', 'aggregation_scheme', 'roles']
+    `['annotations', 'replacement_of', 'aggregation_scheme', 'roles']`
 
     """
     assert isinstance(filename, string_types)
@@ -100,6 +100,9 @@ def function(inputs, outputs=None, mode=None, updates=None, givens=None,
         If True, do not perform any automatic update on Variables. If False
         (default), perform them all. Else, perform automatic updates on all
         Variables that are neither in "updates" nor in "no_default_updates".
+    accept_inplace : bool
+        True iff the graph can contain inplace operations prior to the
+        optimization phase (default is False).
     name : str
         An optional name for this function. The profile mode will print the time
         spent in this function.
@@ -115,10 +118,10 @@ def function(inputs, outputs=None, mode=None, updates=None, givens=None,
         Ops in the graph, an Exception will be raised.
     allow_input_downcast: bool or None
         True means that the values passed as inputs when calling the function
-        can be silently downcasted to fit the dtype of the corresponding
+        can be silently down-casted to fit the dtype of the corresponding
         Variable, which may lose precision. False means that it will only be
         cast to a more general, or precise, type. None (default) is almost like
-        False, but allows downcasting of Python float scalars to floatX.
+        False, but allows down-casting of Python float scalars to floatX.
     profile: None, True, or ProfileStats instance
         Accumulate profiling information into a given ProfileStats instance.
         If argument is `True` then a new ProfileStats instance will be used.
@@ -209,9 +212,9 @@ def function(inputs, outputs=None, mode=None, updates=None, givens=None,
          4. Linker
                The linker uses a Python loop to execute the code associated
                with all the Apply nodes in the graph in the correct order.
-               The CVM is a linker that replaces this Python loop with a C
-               loop to avoid continuously changing between Python and C.
-               The CVM is faster for 2 reasons:
+               The C Virtual Machine (CVM) is a linker that replaces this
+               Python loop with a C loop to avoid continuously changing
+               between Python and C. The CVM is faster for 2 reasons:
                  1) Its internal logic is in C, so no Python interpreter
                     overhead.
                  2) It makes native calls from the VM logic into thunks that
@@ -219,7 +222,6 @@ def function(inputs, outputs=None, mode=None, updates=None, givens=None,
                The VM is a linker that was developed to prototype the CVM. it
         was easier to develop the VM in Python then translate it to C instead
         of just writing it in C from scratch.
-               CVM stands for C Virtual Machine.
 
     """
     if isinstance(outputs, dict):
@@ -252,7 +254,7 @@ def function(inputs, outputs=None, mode=None, updates=None, givens=None,
             func_frame = stack[idx - 1]
             while "theano/gof" in func_frame[0] and idx > 0:
                 idx -= 1
-                # This can hapen if we call var.eval()
+                # This can happen if we call var.eval()
                 func_frame = stack[idx - 1]
             name = func_frame[0] + ':' + str(func_frame[1])
 

theano/compile/function_module.py

@@ -1726,8 +1726,8 @@ def orig_function(inputs, outputs, mode=None, accept_inplace=False,
         Default of None means to use `config.mode` (see below for descriptive
         string list).
     name : str
-        An optional name for this fct. If used, the profile mode will print the
-        time spent in this fct.
+        An optional name for this function. If used, the profile mode will print the
+        time spent in this function.
     accept_inplace : bool
         True iff the graph can contain inplace operations prior to the
         optimization phase (default is False).

theano/compile/mode.py

@@ -18,35 +18,6 @@ from six import string_types
 _logger = logging.getLogger('theano.compile.mode')
 
 
-def check_equal(x, y):
-    """
-    Returns True iff x[0] and y[0] are equal (checks the dtype and shape if x
-    and y are numpy.ndarray instances). Used internally.
-
-    """
-    # I put the import here to allow using theano without scipy.
-    import scipy.sparse as sp
-    x, y = x[0], y[0]
-
-    # TODO: bug in current scipy, two sparse matrices are never equal,
-    # remove when moving to 0.7
-    if sp.issparse(x):
-        x = x.todense()
-    if sp.issparse(y):
-        y = y.todense()
-
-    if isinstance(x, numpy.ndarray) and isinstance(y, numpy.ndarray):
-        if (x.dtype != y.dtype or
-                x.shape != y.shape or
-                numpy.any(abs(x - y) > 1e-10)):
-            raise Exception("Output mismatch.",
-                            {'performlinker': x, 'clinker': y})
-    else:
-        if x != y:
-            raise Exception("Output mismatch.",
-                            {'performlinker': x, 'clinker': y})
-
-
 # If a string is passed as the linker argument in the constructor for
 # Mode, it will be used as the key to retrieve the real linker in this
 # dictionary
@@ -384,7 +355,7 @@ predefined_modes = {'FAST_COMPILE': FAST_COMPILE,
                     'FAST_RUN': FAST_RUN,
                     }
 
-instanciated_default_mode = None
+instantiated_default_mode = None
 
 
 def get_mode(orig_string):
@@ -395,17 +366,17 @@ def get_mode(orig_string):
     if not isinstance(string, string_types):
         return string  # it is hopefully already a mode...
 
-    global instanciated_default_mode
+    global instantiated_default_mode
     # The default mode is cached. However, config.mode can change
-    # If instanciated_default_mode has the right class, use it.
-    if orig_string is None and instanciated_default_mode:
+    # If instantiated_default_mode has the right class, use it.
+    if orig_string is None and instantiated_default_mode:
         if string in predefined_modes:
             default_mode_class = predefined_modes[string].__class__.__name__
         else:
             default_mode_class = string
-        if (instanciated_default_mode.__class__.__name__ ==
+        if (instantiated_default_mode.__class__.__name__ ==
                 default_mode_class):
-            return instanciated_default_mode
+            return instantiated_default_mode
 
     if string in ['Mode', 'ProfileMode', 'DebugMode', 'NanGuardMode']:
         if string == 'DebugMode':
@@ -422,6 +393,7 @@ def get_mode(orig_string):
             # This might be required if the string is 'ProfileMode'
             from .profilemode import ProfileMode  # noqa
             from .profilemode import prof_mode_instance_to_print
+            # TODO: Can't we look up the name and invoke it rather than using eval here?
             ret = eval(string +
                        '(linker=config.linker, optimizer=config.optimizer)')
     elif string in predefined_modes:
@@ -437,7 +409,7 @@ def get_mode(orig_string):
             ret = ret.including(*theano.config.optimizer_including.split(':'))
         if theano.config.optimizer_requiring:
             ret = ret.requiring(*theano.config.optimizer_requiring.split(':'))
-        instanciated_default_mode = ret
+        instantiated_default_mode = ret
 
     # must tell python to print the summary at the end.
     if string == 'ProfileMode':

theano/compile/pfunc.py

@@ -306,6 +306,9 @@ def pfunc(params, outputs=None, mode=None, updates=None, givens=None,
         If False (default), perform them all. Else, perform automatic updates
         on all Variables that are neither in "updates" nor in
         "no_default_updates".
+    accept_inplace : bool
+        True iff the graph can contain inplace operations prior to the
+        optimization phase (default is False).
     name : None or string
         Attaches a name to the profiling result of this function.
     allow_input_downcast : bool

theano/gof/cc.py

@@ -717,7 +717,7 @@ class CLinker(link.Linker):
                               [get_c_declare, get_c_extract_out,
                                   (get_c_sync, get_c_cleanup)]]
             else:
-                raise Exception("what the fuck")
+                raise Exception("this shouldn't be possible, please report this exception")
 
             builder, block = struct_variable_codeblocks(variable, policy,
                                                         id, symbol, sub)